Results

Loops were firstly called using Mustache. Afterwards, a union of significantly called loops in each condition (M1, M4 and NTC) was used for differential analysis using a modified DESeq2 approach via HiCDCPlus. Knockdown samples (M1 and M4) were pooled together.

Download diff_final.csv

PCA

All loops

Top 500 most variable loops

MA plot

Logfold change is MED4KD over NTC

No cutoff

Cutoff = 50

Using a cutoff of 50 normalized mean counts

Cutoff = 100

Using a cutoff of 100 normalized mean counts

Volcano plot